The Coalescence of Intrahost HIV Lineages Under Symmetric CTL Attack

TL;DR

This paper introduces a stochastic ODE model to analyze how cytotoxic T lymphocyte attack influences the coalescence of HIV lineages within a host, providing new insights into immune control mechanisms.

Contribution

It develops a stochastic ODE framework extending deterministic models and links CTL attack to HIV lineage coalescence via a paintbox construction, especially under low HIV population sizes.

Findings

Stochastic model accurately reflects HIV lineages under CTL attack.

Coalescence of HIV lineages can be described by a paintbox construction.

Results connect immune response to HIV lineage structure.

Abstract

Cytotoxic T lymphocytes (CTLs) are immune system cells that are thought to play an important role in controlling HIV infection. We develop a stochastic ODE model of HIV-CTL interaction that extends current deterministic ODE models. Based on this stochastic model, we consider the effect of CTL attack on intrahost HIV lineages assuming CTLs attack several epitopes with equal strength. In this setting, we introduce a limiting version of our stochastic ODE under which we show that the coalescence of HIV lineages can be described by a simple paintbox construction. Through numerical experiments, we show that our results under the limiting stochastic ODE accurately reflect HIV lineages under CTL attack when the HIV population size is on the low end of its hypothesized range. Current techniques of HIV lineage construction depend on the Kingman coalescent. Our results give an explicit connection between CTL attack and HIV lineages.